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Crystal structure of MIRANDA/STAUFEN DSRBD5 complex

Analyse Crystal structure of MIRANDA/STAUFEN DSRBD5 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CFF
Type: protein
Length: 626 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Miranda; Staufen
UniProt: Q9VDR7, P25159
Pockets: 1 · best druggability 0.29

Structure

x-ray diffraction · 7 distinct chains · 77% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Miranda	protein	87	98% helix, 0% strand	Q9VDR7
B	Miranda	protein	88	98% helix, 0% strand	Q9VDR7
C	Miranda	protein	87	95% helix, 0% strand	Q9VDR7
D	Miranda	protein	88	97% helix, 0% strand	Q9VDR7
E, G	Staufen	protein	70	41% helix, 29% strand	P25159
F	Staufen	protein	71	42% helix, 28% strand	P25159
H	Staufen	protein	65	46% helix, 31% strand	P25159

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	74	0.29	0.73	13	empty

Interfaces

12 interfaces between chains.

B–D · 2334 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 2221 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 745 Å² buried · 6 hydrogen bonds · protein-protein
D–G · 741 Å² buried · 9 hydrogen bonds · protein-protein
A–F · 730 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

5CFF · Crystal structure of Miranda/Staufen dsRBD5 complex · the same entry in another collection · chain H against H, TM-score 1.00
P25159 · AlphaFold monomer V2.0 prediction for maternal effect protein staufen (P25159) · a predicted model of the same protein · chain H against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9VDR7
Every structure of UniProt P25159
Elsewhere: RCSB PDB 5CFF · PDBe 5CFF · UniProt Q9VDR7 · UniProt P25159

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